maxStepProb: M-step (maximization w.r.t. initial and transition...

In plbaldoni/epigraHMM: Epigenomic R-based analysis with hidden Markov models

M-step (maximization w.r.t. initial and transition probabilities)

Description

M-step (maximization w.r.t. initial and transition probabilities)

Usage

maxStepProb(hdf5)

Arguments

hdf5	path to where the hdf5 is saved

Examples

#Creating dummy object
countData <- rbind(matrix(rnbinom(1e3,mu = 2,size = 10),ncol = 1),
                  matrix(rnbinom(2e3,mu = 7.5,size = 5),ncol = 1),
                  matrix(rnbinom(1e3,mu = 2,size = 10),ncol = 1))



colData <- data.frame(condition = 'A', replicate = 1)
object <- epigraHMMDataSetFromMatrix(countData,colData)

#Initializing
object <- initializer(object,controlEM())

#Running epigraHMM
object <- epigraHMM(object,controlEM(),type = 'consensus',dist = 'nb')

#Example
maxStepProb(hdf5 = S4Vectors::metadata(object)$output)

plbaldoni/epigraHMM documentation built on Oct. 15, 2023, 7:53 p.m.